SMTL ID : 5cvq.1

Structure of Xoo1075, a peptide deformylase from Xanthomonas oryzae pv oryzae, in complex with actinonin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

6 x CD: CADMIUM ION(Non-covalent)

CD.1: 2 residues within 4Å: Chain A: E.128, E.130 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.128, A:E.130, A:E.130, H2O.1, H2O.2 CD.2: 5 residues within 4Å: Chain A: Q.51, C.99, H.141, H.145 Ligands: BB2.5 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.99, A:H.141, A:H.145 CD.4: 1 residues within 4Å: Chain A: E.132 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.132, A:E.132, H2O.2 CD.6: 2 residues within 4Å: Chain B: E.128, E.130 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.128, B:E.130, B:E.130, H2O.4, H2O.6 CD.7: 5 residues within 4Å: Chain B: Q.51, C.99, H.141, H.145 Ligands: BB2.10 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.99, B:H.141, B:H.145 CD.9: 1 residues within 4Å: Chain B: E.132 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.132, B:E.132, H2O.6

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.3: 7 residues within 4Å: Chain A: L.14, G.148, R.149, L.150, S.153 Chain B: F.158, D.159 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:L.14 Hydrogen bonds: A:L.150, A:S.153 Water bridges: A:S.153, B:F.158 Salt bridges: A:R.149 ACT.8: 7 residues within 4Å: Chain A: F.158, D.159 Chain B: L.14, G.148, R.149, L.150, S.153 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.14 Hydrogen bonds: B:L.150, B:S.153 Water bridges: B:S.153, A:F.158 Salt bridges: B:R.149

2 x BB2: ACTINONIN(Non-covalent)

BB2.5: 18 residues within 4Å: Chain A: H.43, G.44, V.45, G.46, Q.51, W.96, E.97, G.98, C.99, L.100, R.106, F.134, R.137, V.138, H.141, E.142, H.145 Ligands: CD.2 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:E.97, A:L.100, A:F.134, A:R.137, A:V.138 Hydrogen bonds: A:V.45, A:G.46, A:G.46, A:Q.51, A:G.98, A:G.98, A:L.100 BB2.10: 18 residues within 4Å: Chain B: H.43, G.44, V.45, G.46, Q.51, W.96, E.97, G.98, C.99, L.100, R.106, F.134, R.137, V.138, H.141, E.142, H.145 Ligands: CD.7 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:E.97, B:L.100, B:F.134, B:R.137, B:V.138 Hydrogen bonds: B:V.45, B:G.46, B:G.46, B:Q.51, B:G.98, B:G.98, B:L.100

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ngo, H.P.T. et al., Structure of Xoo1075, a peptide deformylase from Xanthomonas oryzae pv oryzae, in complex with actinonin. To Be Published

Release Date

2016-08-03

Peptides

Peptide deformylase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Peptide deformylase

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